title: Operator- and software-related post-experimental variability and source of error in 2-DE analysis.
abstract: In the field of proteomics, several approaches have been developed for separating proteins and analyzing their differential relative abundance. One of the oldest, yet still widely used, is 2-DE. Despite the continuous advance of new methods, which are less demanding from a technical standpoint, 2-DE is still compelling and has a lot of potential for improvement. The overall variability which affects 2-DE includes biological, experimental, and post-experimental (software-related) variance. It is important to highlight how much of the total variability of this technique is due to post-experimental variability, which, so far, has been largely neglected. In this short review, we have focused on this topic and explained that post-experimental variability and source of error can be further divided into those which are software-dependent and those which are operator-dependent. We discuss these issues in detail, offering suggestions for reducing errors that may affect the quality of results, summarizing the advantages and drawbacks of each approach.
authors.affiliation: Division of Metabolism, Department of Clinical and Experimental Medicine, University of Padua, via Giustiniani 2, 35128, Padua, Italy. millionirenato@gmail.com
authors.forename: Renato
authors.initials: R
authors.lastname: Millioni
authors.forename: Lucia
authors.initials: L
authors.lastname: Puricelli
authors.forename: Stefano
authors.initials: S
authors.lastname: Sbrignadello
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Iori
authors.forename: Ellen
authors.initials: E
authors.lastname: Murphy
authors.forename: Paolo
authors.initials: P
authors.lastname: Tessari
mesh_terms: D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D020543:Proteome / Q000032:analysis* / Q000592:standards; D040901:Proteomics / Q000379:methods; D011786:Quality Control; D012984:Software
chemical_list: D020543:Proteome